I too own The MOTU mk3 hybrid and using it with windows has been pretty solid. After about 4 years of use (first for studio work then a dedicated HW interface) it developed 'digital spasm'. The digital input indicator on the front LED panel would bounce up down ill radically after being on for over an hour. This behavior caused the reverb to get hit when the indicator would spike making it sound like thunder (akin to shaking an amplifier with spring reverb). The digital ports (S/PDIF) were empty. Dummy plugs didn't help nor upgrading to the latest firmware. MOTU support was very helpful and suggested as a last resort to perform a hard firmware reset on the unit. That resolved the issue and it's been fine ever since. Had that not worked, the final resolve would have been to send it back to MOTU for repair or replacement for $99.
Yes, I do a full shutdown and start up of my HW rig so that could attribute to my reliability. The only minor beef I have with this unit, as I've mentioned in past threads, is the soft on & off switch embedded in one of the control knobs. I have to manually turn it on each time when starting up. Kind of prevents me from having a "one button on" solution we've discussed in the past. But hey this a home studio install so not really a big deal.
Danny B.